Evaluation of Microbial Populations in Chicken Ceca Raised on Pasture Flock Fed with Commercial Prebiotics via Sequencing (Illumina MiSeq)

Introduction: Prebiotics are non-digestible carbohydrate dietary supplements that stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outside with fresh grass, sunlight and air, which is a different growth conditions with conventional chickens.

Purpose: The purpose of this study was to evaluate the difference of microbial populations in ceca fed with commercial prebiotics derived from brewer’s yeast cell wall via Illumina MiSeq platform.

Methods: A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C, control (no prebiotic); 2) T1, Biolex^® MB40; 3) T2, Leiber^®ExCel, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and extracted ceca for DNA extraction. The Illumina MiSeq platform based on 16s rRNA gene was applied for microbiome analysis.

Results: Both treatments had limited impact on the microbial populations at the phylum level, with a slight decrease in the number of Bacteroides for both treatments and an increase of proteobacteria for the Biolex^® MB40 treatment. Both treatments resulted in significant decreases of members of the Bacteroides genus (53% to 43%), which include species that can be detrimental. This decrease was accompanied with a significant increase of Phascolarcobacterium and Faecalibacterium, both Firmicutes associated with health benefits. The Leiber^® ExCel treatment also induced an increase in Ruminococcus, which is another beneficial genus.

Significance: According to the development of next generation sequencing (NGS), microbiome analysis based on 16s rRNA gene is useful to evaluate the prebiotics effects on poultry gut health as well as pathogenic bacteria prevalence.